bwa mem -w option
does anybody know what is the range of INT that can be used for the -w option of BWA Mem? (-w ) : INTBand width. Essentially, gaps longer than *INT will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. [100]
thanks ib
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Forum: BWA command guide
written by Chen Sun
-
Long terminal gaps in MAFFT alignment
written by Ghoti •
-
Are there maximum gap penalty scores in BWA-MEM?
written by Diploid Progenitor •
-
Post Genome Assembly
written by div •
-
Mapping blast xml report elements to their variable names in biopython
written by Bara'a
-
bwa mem mismatch option
written by Varun Gupta
-
How To Evaluate The Scoring Scheme Used In Pairwise Alignment
written by Maria •
-
How To Adjust Bwa Mem To Allow For Longer Gaps In Contig Alignment
written by William
-
Meaning Of -A In Vcftools Vcfutils.Pl Varfilter?
written by Dan
-
Bwa Gapped Alignment
written by Bioscientist
Just guessing, but isn't this the maximum gap length within a read to be reported in the same hit. Longer than this and the read alignment will be split and reported in a separate hit/line